Starting phenix.real_space_refine on Sun Mar 10 21:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/03_2024/7f6v_31482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/03_2024/7f6v_31482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/03_2024/7f6v_31482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/03_2024/7f6v_31482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/03_2024/7f6v_31482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/03_2024/7f6v_31482_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3526 2.51 5 N 866 2.21 5 O 892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5314 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2629 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2629 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.45, per 1000 atoms: 0.65 Number of scatterers: 5314 At special positions: 0 Unit cell: (94.302, 116.61, 92.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 892 8.00 N 866 7.00 C 3526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 924.9 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 10 through 69 removed outlier: 3.562A pdb=" N ARG A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 100 removed outlier: 4.005A pdb=" N TYR A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 123 through 153 Processing helix chain 'A' and resid 160 through 185 Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.758A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 247 Processing helix chain 'A' and resid 265 through 298 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 304 through 333 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 10 through 69 removed outlier: 3.562A pdb=" N ARG B 34 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 100 removed outlier: 4.005A pdb=" N TYR B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 123 through 153 Processing helix chain 'B' and resid 160 through 185 Processing helix chain 'B' and resid 193 through 209 removed outlier: 3.758A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 247 Processing helix chain 'B' and resid 265 through 298 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 304 through 333 Proline residue: B 313 - end of helix 424 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1596 1.34 - 1.46: 1356 1.46 - 1.58: 2474 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5470 Sorted by residual: bond pdb=" C10 CLR A 401 " pdb=" C9 CLR A 401 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C10 CLR B 401 " pdb=" C9 CLR B 401 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C5 CLR B 401 " pdb=" C6 CLR B 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C5 CLR A 401 " pdb=" C6 CLR A 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C13 CLR A 401 " pdb=" C17 CLR A 401 " ideal model delta sigma weight residual 1.550 1.525 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 5465 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 120 107.07 - 113.80: 3062 113.80 - 120.53: 2336 120.53 - 127.26: 1822 127.26 - 133.98: 64 Bond angle restraints: 7404 Sorted by residual: angle pdb=" C CYS A 68 " pdb=" N LYS A 69 " pdb=" CA LYS A 69 " ideal model delta sigma weight residual 119.78 123.78 -4.00 1.24e+00 6.50e-01 1.04e+01 angle pdb=" C CYS B 68 " pdb=" N LYS B 69 " pdb=" CA LYS B 69 " ideal model delta sigma weight residual 119.78 123.78 -4.00 1.24e+00 6.50e-01 1.04e+01 angle pdb=" C13 CLR A 401 " pdb=" C17 CLR A 401 " pdb=" C20 CLR A 401 " ideal model delta sigma weight residual 119.60 110.29 9.31 3.00e+00 1.11e-01 9.64e+00 angle pdb=" C13 CLR B 401 " pdb=" C17 CLR B 401 " pdb=" C20 CLR B 401 " ideal model delta sigma weight residual 119.60 110.33 9.27 3.00e+00 1.11e-01 9.54e+00 angle pdb=" C LYS B 69 " pdb=" CA LYS B 69 " pdb=" CB LYS B 69 " ideal model delta sigma weight residual 113.04 108.81 4.23 1.63e+00 3.76e-01 6.74e+00 ... (remaining 7399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2954 17.67 - 35.34: 262 35.34 - 53.00: 42 53.00 - 70.67: 8 70.67 - 88.34: 4 Dihedral angle restraints: 3270 sinusoidal: 1422 harmonic: 1848 Sorted by residual: dihedral pdb=" CA LEU B 32 " pdb=" C LEU B 32 " pdb=" N TYR B 33 " pdb=" CA TYR B 33 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LEU A 32 " pdb=" C LEU A 32 " pdb=" N TYR A 33 " pdb=" CA TYR A 33 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU B 304 " pdb=" CG GLU B 304 " pdb=" CD GLU B 304 " pdb=" OE1 GLU B 304 " ideal model delta sinusoidal sigma weight residual 0.00 88.34 -88.34 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 772 0.105 - 0.210: 18 0.210 - 0.315: 2 0.315 - 0.420: 2 0.420 - 0.525: 2 Chirality restraints: 796 Sorted by residual: chirality pdb=" C14 CLR A 401 " pdb=" C13 CLR A 401 " pdb=" C15 CLR A 401 " pdb=" C8 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" C14 CLR B 401 " pdb=" C13 CLR B 401 " pdb=" C15 CLR B 401 " pdb=" C8 CLR B 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" C10 CLR A 401 " pdb=" C1 CLR A 401 " pdb=" C5 CLR A 401 " pdb=" C9 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 793 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 313 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PRO B 313 " 0.025 2.00e-02 2.50e+03 pdb=" O PRO B 313 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE B 314 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 313 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PRO A 313 " -0.025 2.00e-02 2.50e+03 pdb=" O PRO A 313 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 314 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 307 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C VAL A 307 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL A 307 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU A 308 " 0.008 2.00e-02 2.50e+03 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1929 2.86 - 3.37: 5635 3.37 - 3.88: 8482 3.88 - 4.39: 8583 4.39 - 4.90: 14447 Nonbonded interactions: 39076 Sorted by model distance: nonbonded pdb=" O LYS B 332 " pdb=" OG SER B 335 " model vdw 2.356 2.440 nonbonded pdb=" O LYS A 332 " pdb=" OG SER A 335 " model vdw 2.356 2.440 nonbonded pdb=" OG SER B 157 " pdb=" NH1 ARG B 220 " model vdw 2.436 2.520 nonbonded pdb=" OG SER A 157 " pdb=" NH1 ARG A 220 " model vdw 2.436 2.520 nonbonded pdb=" O VAL B 159 " pdb=" N ALA B 162 " model vdw 2.443 2.520 ... (remaining 39071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.810 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.750 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5470 Z= 0.347 Angle : 0.774 9.312 7404 Z= 0.392 Chirality : 0.054 0.525 796 Planarity : 0.003 0.024 904 Dihedral : 13.915 88.339 2074 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.32), residues: 618 helix: 0.94 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -4.45 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.002 0.001 HIS A 283 PHE 0.016 0.001 PHE A 219 TYR 0.016 0.002 TYR B 33 ARG 0.004 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8727 (mtt) cc_final: 0.8420 (ppp) REVERT: A 145 ILE cc_start: 0.8404 (tt) cc_final: 0.8183 (tt) REVERT: A 154 LEU cc_start: 0.8208 (mm) cc_final: 0.7425 (tt) REVERT: A 228 MET cc_start: 0.8435 (ttt) cc_final: 0.7824 (ttm) REVERT: A 239 TYR cc_start: 0.8022 (t80) cc_final: 0.7550 (m-80) REVERT: B 87 MET cc_start: 0.8724 (mtt) cc_final: 0.8420 (ppp) REVERT: B 145 ILE cc_start: 0.8392 (tt) cc_final: 0.8168 (tt) REVERT: B 154 LEU cc_start: 0.8204 (mm) cc_final: 0.7428 (tt) REVERT: B 228 MET cc_start: 0.8434 (ttt) cc_final: 0.7817 (ttm) REVERT: B 239 TYR cc_start: 0.8015 (t80) cc_final: 0.7542 (m-80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2284 time to fit residues: 44.4202 Evaluate side-chains 119 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 330 HIS B 241 GLN B 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5470 Z= 0.197 Angle : 0.587 5.901 7404 Z= 0.291 Chirality : 0.034 0.119 796 Planarity : 0.003 0.032 904 Dihedral : 5.107 33.471 810 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.46 % Allowed : 14.26 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.35), residues: 618 helix: 2.89 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -4.25 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 305 HIS 0.009 0.001 HIS A 330 PHE 0.018 0.001 PHE B 235 TYR 0.012 0.001 TYR A 171 ARG 0.008 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8761 (mtt) cc_final: 0.8447 (ppp) REVERT: A 238 TYR cc_start: 0.7808 (t80) cc_final: 0.7498 (t80) REVERT: A 319 LEU cc_start: 0.8889 (tt) cc_final: 0.8644 (tp) REVERT: B 31 ARG cc_start: 0.9102 (tmm160) cc_final: 0.8867 (ttp80) REVERT: B 87 MET cc_start: 0.8758 (mtt) cc_final: 0.8449 (ppp) REVERT: B 238 TYR cc_start: 0.7790 (t80) cc_final: 0.7483 (t80) REVERT: B 319 LEU cc_start: 0.8894 (tt) cc_final: 0.8647 (tp) outliers start: 14 outliers final: 10 residues processed: 127 average time/residue: 0.1876 time to fit residues: 30.3100 Evaluate side-chains 121 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 330 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5470 Z= 0.198 Angle : 0.567 6.868 7404 Z= 0.285 Chirality : 0.034 0.121 796 Planarity : 0.004 0.037 904 Dihedral : 4.505 30.242 810 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.35 % Allowed : 16.73 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.36), residues: 618 helix: 3.50 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.99 (0.76), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.009 0.001 HIS A 330 PHE 0.014 0.001 PHE B 219 TYR 0.012 0.001 TYR A 171 ARG 0.006 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8800 (mtt) cc_final: 0.8468 (ppp) REVERT: A 100 TYR cc_start: 0.7299 (t80) cc_final: 0.6849 (t80) REVERT: A 237 GLN cc_start: 0.7127 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 238 TYR cc_start: 0.7822 (t80) cc_final: 0.7579 (t80) REVERT: A 319 LEU cc_start: 0.8918 (tt) cc_final: 0.8678 (tp) REVERT: B 87 MET cc_start: 0.8796 (mtt) cc_final: 0.8471 (ppp) REVERT: B 237 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6915 (tm-30) REVERT: B 238 TYR cc_start: 0.7804 (t80) cc_final: 0.7562 (t80) REVERT: B 319 LEU cc_start: 0.8926 (tt) cc_final: 0.8684 (tp) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.1559 time to fit residues: 25.1477 Evaluate side-chains 125 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 330 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5470 Z= 0.158 Angle : 0.530 7.242 7404 Z= 0.263 Chirality : 0.032 0.127 796 Planarity : 0.004 0.036 904 Dihedral : 4.285 30.458 810 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.94 % Allowed : 20.77 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.36), residues: 618 helix: 3.66 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.87 (0.77), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.010 0.001 HIS B 330 PHE 0.021 0.001 PHE A 235 TYR 0.012 0.001 TYR B 171 ARG 0.008 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8810 (mtt) cc_final: 0.8315 (tmm) REVERT: A 319 LEU cc_start: 0.8930 (tt) cc_final: 0.8692 (tp) REVERT: B 87 MET cc_start: 0.8810 (mtt) cc_final: 0.8309 (tmm) REVERT: B 237 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6957 (tm-30) REVERT: B 319 LEU cc_start: 0.8927 (tt) cc_final: 0.8677 (tp) outliers start: 11 outliers final: 10 residues processed: 118 average time/residue: 0.1424 time to fit residues: 22.3310 Evaluate side-chains 118 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.0020 chunk 11 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5470 Z= 0.174 Angle : 0.540 8.281 7404 Z= 0.266 Chirality : 0.033 0.134 796 Planarity : 0.004 0.039 904 Dihedral : 4.028 24.265 810 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.17 % Allowed : 22.18 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.35), residues: 618 helix: 3.70 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.51 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.003 0.001 HIS A 283 PHE 0.013 0.001 PHE A 219 TYR 0.020 0.001 TYR A 238 ARG 0.009 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8814 (mtt) cc_final: 0.8325 (tmm) REVERT: A 309 MET cc_start: 0.5455 (mtt) cc_final: 0.5149 (mtt) REVERT: A 319 LEU cc_start: 0.8931 (tt) cc_final: 0.8685 (tp) REVERT: B 87 MET cc_start: 0.8815 (mtt) cc_final: 0.8307 (tmm) REVERT: B 237 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6954 (tm-30) REVERT: B 309 MET cc_start: 0.5397 (mtt) cc_final: 0.5098 (mtt) REVERT: B 319 LEU cc_start: 0.8932 (tt) cc_final: 0.8675 (tp) outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.1222 time to fit residues: 20.1816 Evaluate side-chains 118 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5470 Z= 0.208 Angle : 0.583 9.017 7404 Z= 0.282 Chirality : 0.033 0.123 796 Planarity : 0.004 0.044 904 Dihedral : 3.936 18.018 810 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.40 % Allowed : 20.95 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.54 (0.35), residues: 618 helix: 3.77 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.50 (0.76), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 210 HIS 0.002 0.000 HIS A 283 PHE 0.021 0.001 PHE A 235 TYR 0.015 0.001 TYR B 238 ARG 0.010 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8811 (mtt) cc_final: 0.8318 (tmm) REVERT: A 319 LEU cc_start: 0.8969 (tt) cc_final: 0.8709 (tp) REVERT: A 327 ARG cc_start: 0.7132 (tpt170) cc_final: 0.6893 (tpt170) REVERT: B 87 MET cc_start: 0.8813 (mtt) cc_final: 0.8304 (tmm) REVERT: B 319 LEU cc_start: 0.8988 (tt) cc_final: 0.8727 (tp) outliers start: 25 outliers final: 15 residues processed: 134 average time/residue: 0.1456 time to fit residues: 26.1317 Evaluate side-chains 125 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5470 Z= 0.169 Angle : 0.567 8.643 7404 Z= 0.273 Chirality : 0.034 0.273 796 Planarity : 0.004 0.038 904 Dihedral : 3.864 20.985 810 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 22.89 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.52 (0.35), residues: 618 helix: 3.76 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.38 (0.77), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.002 0.000 HIS A 283 PHE 0.014 0.001 PHE B 219 TYR 0.016 0.001 TYR B 238 ARG 0.008 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8811 (mtt) cc_final: 0.8300 (tmm) REVERT: A 319 LEU cc_start: 0.8956 (tt) cc_final: 0.8689 (tp) REVERT: A 327 ARG cc_start: 0.7130 (tpt170) cc_final: 0.6924 (tpt170) REVERT: B 87 MET cc_start: 0.8808 (mtt) cc_final: 0.8286 (tmm) REVERT: B 237 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 319 LEU cc_start: 0.8971 (tt) cc_final: 0.8709 (tp) REVERT: B 327 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6921 (tpt170) outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 0.1359 time to fit residues: 22.4967 Evaluate side-chains 117 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 40 optimal weight: 0.0270 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.4646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5470 Z= 0.153 Angle : 0.546 9.022 7404 Z= 0.260 Chirality : 0.033 0.227 796 Planarity : 0.004 0.055 904 Dihedral : 3.731 18.903 810 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.41 % Allowed : 22.36 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.35), residues: 618 helix: 3.72 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.14 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.002 0.000 HIS B 283 PHE 0.023 0.001 PHE B 235 TYR 0.015 0.001 TYR B 238 ARG 0.011 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8792 (mtt) cc_final: 0.8299 (tmm) REVERT: A 319 LEU cc_start: 0.8897 (tt) cc_final: 0.8663 (tp) REVERT: B 87 MET cc_start: 0.8787 (mtt) cc_final: 0.8289 (tmm) REVERT: B 291 LEU cc_start: 0.8667 (tp) cc_final: 0.8376 (tp) REVERT: B 319 LEU cc_start: 0.8955 (tt) cc_final: 0.8695 (tp) outliers start: 8 outliers final: 8 residues processed: 114 average time/residue: 0.1265 time to fit residues: 20.2216 Evaluate side-chains 109 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.0010 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 40 optimal weight: 3.9990 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5470 Z= 0.161 Angle : 0.557 9.066 7404 Z= 0.266 Chirality : 0.033 0.214 796 Planarity : 0.003 0.035 904 Dihedral : 3.677 20.942 810 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.58 % Allowed : 22.01 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.35), residues: 618 helix: 3.76 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.14 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.004 0.001 HIS B 330 PHE 0.013 0.001 PHE B 219 TYR 0.021 0.001 TYR B 238 ARG 0.009 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8774 (mtt) cc_final: 0.8287 (tmm) REVERT: A 188 ARG cc_start: 0.7583 (ppt170) cc_final: 0.7369 (ppt170) REVERT: A 237 GLN cc_start: 0.7264 (tm-30) cc_final: 0.6820 (tm-30) REVERT: A 291 LEU cc_start: 0.8603 (tp) cc_final: 0.8314 (tp) REVERT: A 319 LEU cc_start: 0.8914 (tt) cc_final: 0.8664 (tp) REVERT: B 87 MET cc_start: 0.8770 (mtt) cc_final: 0.8279 (tmm) REVERT: B 188 ARG cc_start: 0.7590 (ppt170) cc_final: 0.7378 (ppt170) REVERT: B 291 LEU cc_start: 0.8648 (tp) cc_final: 0.8370 (tp) REVERT: B 319 LEU cc_start: 0.8969 (tt) cc_final: 0.8701 (tp) outliers start: 9 outliers final: 9 residues processed: 111 average time/residue: 0.1276 time to fit residues: 19.7830 Evaluate side-chains 112 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.0030 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5470 Z= 0.174 Angle : 0.572 9.012 7404 Z= 0.273 Chirality : 0.033 0.205 796 Planarity : 0.003 0.033 904 Dihedral : 3.669 19.701 810 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.58 % Allowed : 22.54 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.35), residues: 618 helix: 3.77 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.09 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.004 0.001 HIS B 330 PHE 0.014 0.001 PHE B 219 TYR 0.024 0.001 TYR A 238 ARG 0.008 0.001 ARG A 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8782 (mtt) cc_final: 0.8288 (tmm) REVERT: A 237 GLN cc_start: 0.7277 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 291 LEU cc_start: 0.8597 (tp) cc_final: 0.8296 (tp) REVERT: A 319 LEU cc_start: 0.8955 (tt) cc_final: 0.8712 (tp) REVERT: B 87 MET cc_start: 0.8775 (mtt) cc_final: 0.8282 (tmm) REVERT: B 188 ARG cc_start: 0.7588 (ppt170) cc_final: 0.7385 (ppt170) REVERT: B 291 LEU cc_start: 0.8658 (tp) cc_final: 0.8374 (tp) REVERT: B 319 LEU cc_start: 0.8976 (tt) cc_final: 0.8705 (tp) outliers start: 9 outliers final: 9 residues processed: 112 average time/residue: 0.1540 time to fit residues: 24.0251 Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.169363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129049 restraints weight = 8707.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.133134 restraints weight = 4266.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.135695 restraints weight = 2853.051| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5470 Z= 0.178 Angle : 0.573 8.917 7404 Z= 0.273 Chirality : 0.034 0.198 796 Planarity : 0.003 0.031 904 Dihedral : 3.673 19.391 810 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.94 % Allowed : 22.01 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.64 (0.35), residues: 618 helix: 3.78 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.04 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.007 0.001 HIS B 330 PHE 0.020 0.001 PHE A 322 TYR 0.025 0.001 TYR A 238 ARG 0.008 0.001 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.19 seconds wall clock time: 24 minutes 55.54 seconds (1495.54 seconds total)